Hi Roz - as you guess, very difficult to diagnose without actually seeing the problem - but the whole security level thing is based around that you can actually write some pretty effective viruses using Visual Basic for Excel, so the warning message is useful for protecting your computer in that way.
Regarding some of your problems however, by way of explanation - Microsoft changed the way Excel saves files for Office 2007 (not to be confused with Vista) and that is why it is saved as a .xlms file. You can get it to save as an Office 2003 document by going to the file menu, selecting "save as.." and in the file type drop-down choosing excel 2003 spreadsheet.
The problem with the analytical toolkit your friend is trying to work with is that there may be an add-on to excel that you have not added, or in the visual basic code the appropriate reference is not added. I doubt it is a compatibility problem between versions, if it were - you would receive a message trying to convert your spreadsheet to the latest version. My guess is that your friend needs to install the toolkit. The reason why it is saying hidden module, is that the toolkit will be a compiled version of the code (which essentially means uneditable) and if the spreadsheet is trying to reference something in it - it will not be able to.
Sorry I cant be of more help, but I hope this explains a few things.